NEWS

---

MicrobiomeR 0.8.0

• Fixed heat-tree rank generation so each rank is filtered independently and nodes are sized by retained descendant OTU counts.
• Clarified the heat-tree node-size interpretation in the package documentation.
• Removed the outdated lab location and improved documentation readability.
• Restored stacked barplot sample labels and removed y-axis baseline padding (#109).
• Completed package citation metadata and usage guidance (#33).
• Made the .rda input-validation test independent of the test working directory.
• Reduced routine test and vignette build time with deterministic, clearly labeled example-data subsets while preserving the full exported datasets.

MicrobiomeR 0.6.2

• Added compatibility shims for upstream metacoder/taxa API drift, including a local parse_phyloseq() fallback for the upstream ranks_ref bug and removal of stale modes and taxa import paths.

MicrobiomeR 0.6.1

• Added StagedInstall: false to DESCRIPTION file.

MicrobiomeR 0.6.0

• Improved documentation of ordination methods and distances.
• Deprecated select_otu_table parameter for alpha_diversity_plot.
• Added site deployment key to travis-ci.com
• Migrated continuous integration to travis-ci.com
• Fixed height of stat comparisons.

MicrobiomeR 0.5.2

• Ran devtools::spell_check() on the package to fix spelling.
• Added deployment of pkgdown site to .travis.yml.

MicrobiomeR 0.5.1

• A specific bug was introduced that prevented local machines and Travis CI servers from building the package.
  • This bug is attributed to a dplyr update (0.7.8 -> 0.8.0.1)
  • See Joss branch #79
  • See Joss debug branch #82
  • See dplyr issue #4213
  • See Travis CI forum post
• Updated the paper for submission

MicrobiomeR 0.5.0

• Added the JOSS paper and draft vignette
• Changed correlation plots
  • Removed color from background
  • Removed hard coded plot limits
  • Added "1:1" line and Average lines
  • Added a trans parameter to transform the x and y axis
• Changed function names
  • From create_metacoder to create_taxmap
  • From agglomerate_metacoder to agglomerate_taxmap
  • From melt_metacoder to melt_taxmap
• Bugs
  • Fixed output_dir bug where error should have been a warning
  • Fixed correlation plot bug where treatments were on the wrong axis.
  • Fixed output message for heat tree plots.
• Fixed build-check Notes and Warnings

MicrobiomeR 0.4.1

• Fixed wilcoxon pvalue in analysis vignette.
• Updated default color palette for stacked_barplot function.

MicrobiomeR 0.4.0

Renamed functions

• get_alpha_diversity_measures to alpha_diversity_measures

Added functions

• Added stacked_barplots, alpha_diversity_plots, ordination_plots
• Added save_stacked_barplots, save_alpha_diversity_plots, save_ordination_plots

Deprecated functions

• Removed save_barplot

• Updated vignettes.

MicrobiomeR 0.3.1

• Added code coverage.

MicrobiomeR 0.3.0

• Changed function names
  • From get_treatment_matrix to treatment_matrix
  • From get_output_dir to output_dir
  • From get_correlation_plots to correlation_plots
  • From get_correlation_data to correlation_data
  • From get_plot_limits to plot_limits
  • From get_heat_tree_plots to heat_tree_plots
  • From get_heat_tree_parameters to heat_tree_parameters
  • From object_handler to create_metacoder

MicrobiomeR 0.2.4

• Added new tests
  • Correlation plot tests
  • Heat tree tests
  • Metacoder Formatting tests
  • Phyloseq tests

MicrobiomeR 0.2.3

Documentation Updates

• Updated documentation for create_pub_table function.

Tests Added

• Added tests for utils.R

MicrobiomeR 0.2.2

Functional Changes

• Added support for multiple treatments for some plots
  • get_heat_tree_plots now produces a metacoder::heat_tree_matrix.
  • correlation_plot now produces multiple plots for data with more that 2 treatments.
  • Added the get_treatment_matrix function
  • Added the get_correlation_data function
• Updated analysis vignette to demonstrate more than 2 treatment groups.
• Updated internal data files.
  • Added new metadata file with 3 treatment groups (nephele_metadata3.txt).
  • Formatted Treatment Group metadata.
• Updated public datasets.
  • Removed Greengenes datasets.
  • Added Silva data with 3 treatment groups.
• Added the color-palettes vignette.

MicrobiomeR 0.2.1

Features Added

• Added permanova function for generating permanova stats.
• Added top_coefficients_barplot for generating a plot of the top coefficients output from the permanova function.

Tests Added

• Added tests for permanova.R.

MicrobiomeR 0.2.0

Documentation Updates

• Added vignettes to package and pkgdown config.
  • About
  • Introduction
  • Data Wrangling
  • Filtering
  • Analysis
• Added reference sections to pkgdown config corresponding to @family tag.
  • Import
  • Formatting
  • Validation
  • Filtering (Basic, Advanced, Other)
  • Visualization
  • Color Palettes

Functional Changes

• Renamed sample_filter to sample_id_filter.
• Renamed get_phyloseq_obj to create_phyloseq.
• Renamed format_metacoder_object to as_custom_format.
• Updated vlookup and get_color_palette parameters.
• Added the root_phyloseq_tree function.
• Fixed minor bugs in code and docs.

MicrobiomeR 0.1.3

• Added custom css for pkgdown.
• Added more sections including authors and vignettes to _pkgdown.yml.
• Fixed @importFrom sections for crayon.

MicrobiomeR 0.1.2

• Added ordination.R for ordination plots.
• Added tests for ordination plots.

MicrobiomeR 0.1.1

• Added logging and better warning messages.

MicrobiomeR 0.1.0

• Changed to a semantic versioning scheme.
• Added barplot.R file of stacked barplot functions.
• Improved get_alpha_diversity_measures function.
• Added a NEWS.md file to track changes to the package.
• Added simple tests for stacked_barplot and alpha_diversity_plot.

MicrobiomeR 0.0.9.2

• Fixes to heat tree plots

MicrobiomeR 0.0.9.1

• Added barplot.R file of stacked barplot functions.